Trends in honey bee toxicity of pesticides used in United States corn and soybean production
updated 2022-12-29
Load data from files:
library(tidyverse)
library(cowplot)
library(readxl)
library(openxlsx)
library(plotly)
library(rcartocolor)
### Load Kynnetec AgroTrak pesticide data (proprietary):
AgroTrak.CornSoy.dat <- read_excel("AgroTrak_CornSoy_v1.xlsx",
skip = 5) %>%
select(Year, Crop,
Type = "Pesticide Type",
Active.Ingredient = "Active Ingredient",
Volume.lbs = "AI volume\r\n(lb)",
Base.Area.Treated = "Base Area Treated\r\n(acres)") %>%
mutate(ai = str_replace_all(Active.Ingredient, " \\(.\\)", ""))
glimpse(AgroTrak.CornSoy.dat)
### Load concordance file:
srcTab <- read_csv("cclistInEcotox.csv")
glimpse(srcTab)
### Load honey bee toxicity values from ecotox export:
ecotox.dat0 <-
read_excel("ECOTOX-Terrestrial-Export_20211207_plusManualAdd.xlsx",
sheet = "Terrestrial-Export") %>%
rename(cas.number = "CAS Number", chemName = "Chemical Name")
### Pare down ecotox values to those likely to be used in this analysis
### (leaving the full ecotox.dat0 just in case needed later),
### and join with the concordance list containing AgroTrak names:
ecotox.dat <- ecotox.dat0 %>%
select(source,
cas.number,
ConcType = `Conc 1 Type (Author)`,
Effect,
LifeStage = `Organism Lifestage`,
ExposureType = `Exposure Type`,
Endpoint,
ObservedDuration.d = `Observed Duration (Days)`,
ObsRespMean = `Observed Response Mean`,
ToxUnit = `Observed Response Units`) %>%
filter(Endpoint %in% c("LD50", "NOEL")) %>%
right_join(srcTab) %>%
select(-inEcoTox, -inManualAdd, -CompTox.PREFERRED_NAME)
glimpse(ecotox.dat) Create a ranked list of pesticides by volume applied in AgroTrak:
AgroTrak.Ranked <- AgroTrak.CornSoy.dat %>%
group_by(Type, ai) %>%
summarize(Volume.lbs = round(sum(Volume.lbs, na.rm = TRUE)),
Base.Area.Treated.sum = round(sum(Base.Area.Treated,
na.rm = TRUE)),
nYears = length(unique(Year)),
Base.Area.perYear = round(Base.Area.Treated.sum / nYears),
Volume.perYear = round(Volume.lbs / nYears)) %>%
arrange(Type, -Volume.lbs)Adult Contact LD50
AdultContactLD50 <- ecotox.dat %>%
filter(LifeStage == "Adult" &
ExposureType == "Dermal" &
Endpoint == "LD50") %>%
group_by(ai) %>%
mutate(checkAI = any(grepl("AI|ai|ae", ToxUnit)),
hasAI = grepl("AI|ai|ae", ToxUnit)) %>%
group_by(ai, hasAI) %>%
mutate(min.d.grp = min(abs(2 - ObservedDuration.d) + 2,
na.rm = TRUE)) %>%
filter(case_when(checkAI == TRUE ~
hasAI == TRUE & ObservedDuration.d <= min.d.grp + 2,
checkAI == FALSE ~
ObservedDuration.d <= min.d.grp + 2)) %>%
ungroup() %>%
select(-checkAI, -hasAI, -min.d.grp) %>%
group_by(ai) %>%
slice(which.min(ObsRespMean))
glimpse(AdultContactLD50)
unique(AdultContactLD50$ConcType)
unique(AdultContactLD50$ToxUnit)
AgroTrak.AdultContactLD50.Rank <- left_join(AgroTrak.Ranked, AdultContactLD50)
#write.xlsx(AgroTrak.AdultContactLD50.Rank,
# file = "Draft_AdultContactLD50.xlsx", asTable = TRUE)
AdultContactLD50.summary <- AgroTrak.AdultContactLD50.Rank %>%
group_by(Type) %>%
mutate(totalVol = sum(Volume.lbs),
pctVol = Volume.lbs / totalVol * 100,
toxVal = !is.na(ObsRespMean)) %>%
#select(Type, ai, Volume.lbs, totalVol, pctVol, toxVal)
group_by(Type, toxVal) %>%
summarize(toxPct = sum(pctVol)) %>%
pivot_wider(names_from = toxVal,
values_from = toxPct) %>%
rename("missing Tox value" = `FALSE`,
"Tox value present" = `TRUE`)knitr::kable(AdultContactLD50.summary, digits = 1)| Type | missing Tox value | Tox value present |
|---|---|---|
| Fungicide | 6.0 | 94.0 |
| Herbicide | 3.4 | 96.6 |
| Insecticide | 8.3 | 91.7 |
Analysis of Adult Contact LD50 RQs for Corn & Soybean
List of active ingredients that made up greater than 1% of a group’s volume in any single year but has no adult dermal LD50 value:
CornSoyAdultContact.dat %>%
filter(is.na(RQ.pctOfType) & Volume.pctOfType > 1) %>%
distinct(Type, ai) %>%
arrange(Type)## # A tibble: 17 x 2
## Type ai
## <chr> <chr>
## 1 Fungicide SULFUR
## 2 Fungicide TEBUCONAZOLE
## 3 Fungicide COPPER SULFATE
## 4 Fungicide TETRACONAZOLE
## 5 Fungicide FLUSILAZOLE
## 6 Fungicide PETROLEUM OIL
## 7 Fungicide PHOSPHORIC ACID
## 8 Herbicide CYANAZINE
## 9 Herbicide ACIFLUORFEN
## 10 Herbicide BENTAZONE
## 11 Herbicide FOMESAFEN
## 12 Herbicide SULFOSATE
## 13 Herbicide GLUFOSINATE
## 14 Herbicide DIMETHENAMID-P
## 15 Insecticide TEBUPIRIMPHOS
## 16 Insecticide BIFENTHRIN
## 17 Insecticide ZETA-CYPERMETHRINFigures
Total pesticide volume applied.
Pesticide volume applied per treated acre.
Summed honey bee risk quotient values for all pesticides.
Summed honey bee risk quotient values per treated acre.
Same RQ plots, faceted & scaled to see fungicide & herbicide trends.
Next steps:
- Since Adult Contact LD50 is the only tox group with sufficient data
to evaluate overall trends, we should focus on that.
- Determine if we can find any additional missing tox data for this endpoint.
- Look at proportion of total RQ contributed by each pesticide to identify largest contributors.
- Look back in AgroTrak data to determine if there are obvious pests driving use of those products - thos seem like targets for non-chemical management research.
## `summarise()` regrouping output by 'Crop', 'Type' (override with `.groups`
## argument)`summarise()` regrouping output by 'Year', 'Crop', 'Type' (override
## with `.groups` argument)## Rows: 1,248
## Columns: 7
## Groups: Year, Crop, Type [116]
## $ Year <dbl> 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, 1998, …
## $ Crop <chr> "Corn", "Corn", "Corn", "Corn", "Corn", "Corn", "Corn"…
## $ Type <chr> "Herbicide", "Herbicide", "Herbicide", "Herbicide", "H…
## $ ai.top <chr> "2,4-D", "ACETOCHLOR", "ALACHLOR", "ATRAZINE", "DICAMB…
## $ BeeREX.RQ <dbl> 446199.10, 463729.70, 591170.16, 1927358.29, 165447.57…
## $ BeeREX.RQ.acre <dbl> 0.07176011, 0.02434560, 0.15482690, 0.03452120, 0.0101…
## $ RQ.pctOfType <dbl> 7.6780180, 7.9796776, 10.1726227, 33.1652207, 2.846956…Insecticides used since 2005:
Corn Insecticides:
| Crop | Type | ai | VolumeContrib | RQContrib | Diff.11 |
|---|---|---|---|---|---|
| Corn | Insecticide | FIPRONIL | 1.0 | 21.1 | 20.1 |
| Corn | Insecticide | CHLORPYRIFOS | 24.5 | 38.8 | 14.3 |
| Corn | Insecticide | PERMETHRIN | 1.4 | 11.9 | 10.5 |
| Corn | Insecticide | CYHALOTHRIN-LAMBDA | 1.6 | 9.3 | 7.7 |
| Corn | Insecticide | DELTAMETHRIN | 0.0 | 6.2 | 6.2 |
| Corn | Insecticide | CYFLUTHRIN | 0.8 | 5.3 | 4.5 |
| Corn | Insecticide | CYHALOTHRIN-GAMMA | 0.0 | 1.5 | 1.5 |
| Corn | Insecticide | ESFENVALERATE | 0.1 | 1.2 | 1.1 |
| Corn | Insecticide | ALPHA-CYPERMETHRIN | 0.1 | 0.9 | 0.8 |
| Corn | Insecticide | CHLORETHOXYFOS | 0.7 | 1.5 | 0.8 |
| Corn | Insecticide | INDOXACARB | 0.2 | 0.9 | 0.7 |
| Corn | Insecticide | TEFLUTHRIN | 8.2 | 8.7 | 0.5 |
| Corn | Insecticide | DIMETHOATE | 1.7 | 2.1 | 0.4 |
| Corn | Insecticide | IMIDACLOPRID | 0.1 | 0.5 | 0.4 |
| Corn | Insecticide | ABAMECTIN | 0.0 | 0.3 | 0.3 |
| Corn | Insecticide | SPINETORAM | 0.0 | 0.2 | 0.2 |
| Corn | Insecticide | CYPERMETHRIN | 0.1 | 0.2 | 0.1 |
| Corn | Insecticide | ACETAMIPRID | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | AZADIRACHTIN | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | CYFLUMETOFEN | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | DISULFOTON | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | FLUPYRADIFURONE | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | MALATHION | 0.2 | 0.2 | 0.0 |
| Corn | Insecticide | METALDEHYDE | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | PIPERONYL BUTOXIDE | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | PYRETHRINS | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | ROTENONE | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | SPINOSYN | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | SULFOXAFLOR | 0.0 | 0.0 | 0.0 |
| Corn | Insecticide | CHLORANTRANILIPROLE | 0.1 | 0.0 | -0.1 |
| Corn | Insecticide | DIAZINON | 0.1 | 0.0 | -0.1 |
| Corn | Insecticide | FENPYROXIMATE | 0.1 | 0.0 | -0.1 |
| Corn | Insecticide | FLUBENDIAMIDE | 0.1 | 0.0 | -0.1 |
| Corn | Insecticide | METHOXYFENOZIDE | 0.1 | 0.0 | -0.1 |
| Corn | Insecticide | METHOMYL | 0.2 | 0.0 | -0.2 |
| Corn | Insecticide | CARBARYL | 0.4 | 0.1 | -0.3 |
| Corn | Insecticide | ETOXAZOLE | 0.4 | 0.0 | -0.4 |
| Corn | Insecticide | PHORATE | 0.5 | 0.0 | -0.5 |
| Corn | Insecticide | METHYL PARATHION | 1.3 | 0.7 | -0.6 |
| Corn | Insecticide | ETHOPROPHOS | 0.9 | 0.1 | -0.8 |
| Corn | Insecticide | HEXYTHIAZOX | 0.8 | 0.0 | -0.8 |
| Corn | Insecticide | ACEPHATE | 1.7 | 0.3 | -1.4 |
| Corn | Insecticide | SPIROMESIFEN | 1.4 | 0.0 | -1.4 |
| Corn | Insecticide | CARBOFURAN | 5.5 | 4.0 | -1.5 |
| Corn | Insecticide | SULFUR | 4.4 | 0.0 | -4.4 |
| Corn | Insecticide | TERBUFOS | 8.7 | 0.4 | -8.3 |
| Corn | Insecticide | PROPARGITE | 30.8 | 0.1 | -30.7 |
| Corn | Insecticide | BACILLUS THURINGIENSIS | 0.2 | NaN | NaN |
| Corn | Insecticide | BIFENTHRIN | 6.7 | NaN | NaN |
| Corn | Insecticide | HARPIN PROTEIN | 0.0 | NaN | NaN |
| Corn | Insecticide | TEBUPIRIMPHOS | 6.9 | NaN | NaN |
| Corn | Insecticide | ZETA-CYPERMETHRIN | 0.3 | NaN | NaN |
Soybean Insecticides:
| Crop | Type | ai | VolumeContrib | RQContrib | Diff.11 |
|---|---|---|---|---|---|
| Soybeans | Insecticide | CYHALOTHRIN-LAMBDA | 6.2 | 17.8 | 11.6 |
| Soybeans | Insecticide | DELTAMETHRIN | 0.1 | 6.0 | 5.9 |
| Soybeans | Insecticide | ESFENVALERATE | 1.0 | 5.8 | 4.8 |
| Soybeans | Insecticide | CYFLUTHRIN | 1.5 | 5.6 | 4.1 |
| Soybeans | Insecticide | THIAMETHOXAM | 0.7 | 4.4 | 3.7 |
| Soybeans | Insecticide | CYHALOTHRIN-GAMMA | 0.2 | 3.5 | 3.3 |
| Soybeans | Insecticide | PERMETHRIN | 0.8 | 3.5 | 2.7 |
| Soybeans | Insecticide | SPINOSYN | 0.0 | 1.7 | 1.7 |
| Soybeans | Insecticide | ABAMECTIN | 0.0 | 1.1 | 1.1 |
| Soybeans | Insecticide | ALPHA-CYPERMETHRIN | 0.2 | 1.0 | 0.8 |
| Soybeans | Insecticide | IMIDACLOPRID | 1.6 | 2.3 | 0.7 |
| Soybeans | Insecticide | SPINETORAM | 0.2 | 0.8 | 0.6 |
| Soybeans | Insecticide | FIPRONIL | 0.0 | 0.6 | 0.6 |
| Soybeans | Insecticide | CLOTHIANIDIN | 0.1 | 0.6 | 0.5 |
| Soybeans | Insecticide | INDOXACARB | 0.2 | 0.3 | 0.1 |
| Soybeans | Insecticide | AFIDOPYROPEN | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | ETOXAZOLE | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | PIPERONYL BUTOXIDE | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | PYRETHRINS | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | ROTENONE | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | SULFOXAFLOR | 0.2 | 0.2 | 0.0 |
| Soybeans | Insecticide | TRALOMETHRIN | 0.0 | 0.0 | 0.0 |
| Soybeans | Insecticide | CYPERMETHRIN | 0.3 | 0.2 | -0.1 |
| Soybeans | Insecticide | ACETAMIPRID | 0.1 | 0.0 | -0.1 |
| Soybeans | Insecticide | DICROTOPHOS | 0.1 | 0.0 | -0.1 |
| Soybeans | Insecticide | FLUPYRADIFURONE | 0.1 | 0.0 | -0.1 |
| Soybeans | Insecticide | NOVALURON | 0.1 | 0.0 | -0.1 |
| Soybeans | Insecticide | CARBOFURAN | 0.4 | 0.2 | -0.2 |
| Soybeans | Insecticide | DIFLUBENZURON | 0.2 | 0.0 | -0.2 |
| Soybeans | Insecticide | METHOMYL | 0.2 | 0.0 | -0.2 |
| Soybeans | Insecticide | DIMETHOATE | 0.7 | 0.4 | -0.3 |
| Soybeans | Insecticide | METHYL PARATHION | 0.7 | 0.3 | -0.4 |
| Soybeans | Insecticide | MALATHION | 1.3 | 0.9 | -0.4 |
| Soybeans | Insecticide | THIODICARB | 0.5 | 0.0 | -0.5 |
| Soybeans | Insecticide | METHOXYFENOZIDE | 0.6 | 0.0 | -0.6 |
| Soybeans | Insecticide | BIFENAZATE | 0.9 | 0.0 | -0.9 |
| Soybeans | Insecticide | CARBARYL | 1.5 | 0.2 | -1.3 |
| Soybeans | Insecticide | FLUBENDIAMIDE | 1.6 | 0.0 | -1.6 |
| Soybeans | Insecticide | PHORATE | 1.7 | 0.0 | -1.7 |
| Soybeans | Insecticide | ALDICARB | 3.1 | 1.1 | -2.0 |
| Soybeans | Insecticide | CHLORANTRANILIPROLE | 2.2 | 0.0 | -2.2 |
| Soybeans | Insecticide | CHLORPYRIFOS | 47.7 | 45.2 | -2.5 |
| Soybeans | Insecticide | SULFUR | 3.0 | 0.0 | -3.0 |
| Soybeans | Insecticide | CHLOROPICRIN | 4.8 | 0.0 | -4.8 |
| Soybeans | Insecticide | DICHLOROPROPENE | 8.4 | 0.0 | -8.4 |
| Soybeans | Insecticide | ACEPHATE | 23.6 | 2.3 | -21.3 |
| Soybeans | Insecticide | BACILLUS THURINGIENSIS | 0.1 | NaN | NaN |
| Soybeans | Insecticide | BIFENTHRIN | 7.1 | NaN | NaN |
| Soybeans | Insecticide | HARPIN PROTEIN | 0.0 | NaN | NaN |
| Soybeans | Insecticide | POLYHEDROSIS VIRUS | 0.1 | NaN | NaN |
| Soybeans | Insecticide | ZETA-CYPERMETHRIN | 0.7 | NaN | NaN |